Rebuilding will probably be cheapest. You could get a kick ass long block from LC, but that would leave you with little or no money left for stuff like new coolant hoses or maybe a starter or alternator, or a new clutch or something. If you do rebuild, you could bore the block oversize .060" and get a stroker crank, street head, and cam from LC. That oughtta give you more power and more torque.
As far as oversized throttle bodies and headers, it's my opinion that they can give you significant increases, but to get full effect you have to upgrade both intake AND exhaust together. For example, if you add a big bore TB with a stock iron exhaust manifold, you may get an increase of like 2 HP, not really noticable. Likewise if you add a header with a stock TB, you may get an extra 5 HP, again, not really noticable. But, if you add both a big throttle body AND a header, you may net a 15 or 20 HP increase. Thats because the header and TB work together to get the maximum effect from eachother. The header lets the TB breathe better and the TB lets the header breathe better. LC sells what they call the "EFI Power Pack" for around $900. It comes with a stainless header, big bore TB, camshaft, and K&N conical airfilter. They claim increases around 25-30 HP on a 22re. 30 horses is pretty good for $900, on a 22re that's like a 26% increase, and should be very noticable on the 'ole seat-of-the-pants meter.
but have you, and YOU PERSONALLY, done this?
I know I did something similar. I tried the tricks with the header, the cam, the fancy air filter, rebuilt the head with bigger valves, the works. I know they didn't work as well as promised on bulletin boards. header was not worth $230 of my money, the air filter was not worth $50 of my money. the cam might have been worth $80 of my money. sometimes "performance" isn't a more-or-less question: " do you ahve more performance than you did before?" somtimes it's a yes-or-no question "does it performe well enough to start every time you turn the key" and for that kind of performance, you either use as many stock toyota parts as you can, or you open the checkbook and start from scratch. the snake oil tricks don't help. I tried ot both ways, I know.